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PL and GQ

Definition
AI-generated

PL and GQ are complementary VCF FORMAT fields for a sample at a variant site.

Topics
Sequencing Data Analysis Formats
Related
Genotype Genotype likelihood Genotype quality (GQ)

Why it matters in GWAS

Together, PL and GQ determine how much confidence to place in hard genotype calls when building cohort VCFs, masking low-confidence genotypes, or exporting to dosage-based formats for association software.

Example usage

"After joint calling, we QC’d FORMAT PL and GQ together: genotypes with GQ < 20 were set to missing once PL supported the reported GT."

Genotype Genotype likelihood Genotype quality (GQ) Phred-scaled genotype likelihoods (PL) Phred quality score Variant Call Format (VCF)
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Danecek P, et al. (2021). Twelve years of SAMtools and BCFtools. Gigascience.
  • HTS specifications: VCF. https://samtools.github.io/hts-specs/
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